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cluster:164 [2017/11/16 12:41]
hmeij07 [PPMA Bench] 		cluster:164 [2018/09/21 07:59] (current)
hmeij07
Line 106: Line 106:
 nvidia-smi -pm 0; nvidia-smi -c 0 nvidia-smi -pm 0; nvidia-smi -c 0
 # gpu_id is done via CUDA_VISIBLE_DEVICES # gpu_id is done via CUDA_VISIBLE_DEVICES
-export CUDA_VISIBLE_DEVCES=$STRING_2+export CUDA_VISIBLE_DEVICES=$STRING_2
 # on n78 # on n78
 /usr/local/mpich-3.1.4/bin/mpirun -launcher ssh -f /home/hmeij/amber/nucleosome/hostfile \ /usr/local/mpich-3.1.4/bin/mpirun -launcher ssh -f /home/hmeij/amber/nucleosome/hostfile \
Line 195: Line 195:
 Mapping of GPU IDs to the 16 PP ranks in this node: 0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3 Mapping of GPU IDs to the 16 PP ranks in this node: 0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3
 Performance:       19.814        1.211 (x16 = 317.024) Performance:       19.814        1.211 (x16 = 317.024)
 +
 +# UPDATE Gromacs 2018, check out these new performance stats for -n 4, -gpu=4
 +
 +# K20, redone with cuda 9
 +
 +root@cottontail gpu]# egrep 'ns/day|Performance' 0[0-4]/md.log
 +01/md.log:                 (ns/day)    (hour/ns)
 +01/md.log:Performance:       74.275        0.323
 +02/md.log:                 (ns/day)    (hour/ns)
 +02/md.log:Performance:       74.111        0.324
 +03/md.log:                 (ns/day)    (hour/ns)
 +03/md.log:Performance:       73.965        0.324
 +04/md.log:                 (ns/day)    (hour/ns)
 +04/md.log:Performance:       74.207        0.323
 +
 +# GTX1080 cuda 8
 + 
 +[hmeij@cottontail gpu]$ egrep 'ns/day|Performance' 0[1-4]/md.log
 +01/md.log:                 (ns/day)    (hour/ns)
 +01/md.log:Performance:      229.229        0.105
 +02/md.log:                 (ns/day)    (hour/ns)
 +02/md.log:Performance:      221.936        0.108
 +03/md.log:                 (ns/day)    (hour/ns)
 +03/md.log:Performance:      217.618        0.110
 +04/md.log:                 (ns/day)    (hour/ns)
 +04/md.log:Performance:      228.854        0.105
 +
 +Almost 900 ns/day for a single server.
  
 </code> </code>
Line 668: Line 696:
  
  
 +==== FreeSurfer ====
  
 +
 +  * http://freesurfer.net/fswiki/DownloadAndInstall#TestyourFreeSurferInstallation
 +  * Example using sample-001.mgz
 +
 +<code>
 +
 +Node n37 (mwgpu cpu run)
 +(2013) Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz
 +recon-all -s bert finished without error
 +example 1 user    0m3.516s
 +example 2 user    893m1.761s ~15 hours
 +example 3 user    ???m       ~15 hours (estimated)
 +
 +Node n78 (amber128 cpu run)
 +(2017) Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
 +recon-all -s bert finished without error
 +example 1 user    0m2.315s
 +example 2 user    488m49.215s ~8 hours
 +example 3 user    478m44.622s ~8 hours
 +
 +
 +freeview -v \
 +    bert/mri/T1.mgz \
 +    bert/mri/wm.mgz \
 +    bert/mri/brainmask.mgz \
 +    bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
 +    -f \
 +    bert/surf/lh.white:edgecolor=blue \
 +    bert/surf/lh.pial:edgecolor=red \
 +    bert/surf/rh.white:edgecolor=blue \
 +    bert/surf/rh.pial:edgecolor=red
 +
 +
 +</code>
 +
 +Development code for the GPU http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
 + 
 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
cluster/164.1510854108.txt.gz ยท Last modified: 2017/11/16 12:41 by hmeij07

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